Analytical Report
SS200000154TR_F5
  • Summary
  • Square Bin
  • Cell Bin
  • Image
Spatial Gene Expression Distribution
Spatial gene expression distribution plot shows MID count at each spot (bin200)
Tissue Plot with Spot (bin200) Colored by MID Count
1,299,371,915
Total Reads
28,830
Mean MID per Bin200
5,005
Mean Gene per Bin200
36,271,914
Unique Reads
Key Metrices
Total Reads
Total number of sequenced reads
Valid CID Reads
Number of reads with CIDs matching the mask file and with MIDs passing QC
Invalid CID Reads
Number of reads with CIDs that cannot be matched with the mask file
Discarded MID Reads
Number of reads with MID that have been discarded since MID sequence quality does not satisfy with further analysis
Clean Reads
Number of Valid CID Reads that have passed QC
Non-Relevant Short Reads
Number of non-relevant short reads
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Annotated Reads
Number of reads that are aligned to transcripts of at least one gene
Unannotated Reads
Number of reads that cannot be aligned to transcript of one gene
Total Reads
100%
1,299,371,915
Valid CID Reads
77.1%
1,002,113,195
Clean Reads
85.1%
852,423,959
Uniquely Mapped Reads
65.7%
560,226,716
Annotated Reads
74.8%
419,110,974
Unique Reads
8.7%
36,271,914
Sequencing Saturation
91.3%
382,839,060
Unannotated Reads
25.2%
141,115,742
Multi-Mapped Reads
24.8%
211,588,387
Unmapped Reads
9.5%
80,608,856
Non-Relevant Short Reads
14.9%
149,689,236
Invalid CID Reads
20.9%
271,798,958
Discarded MID Reads
2.0%
25,459,762
Information
Sequencing
Total Reads
Total number of sequenced reads
Total Q30
Ratio of bases with quality value exceeded 30 in the sequenced reads
CID Q30
Ratio of CID (Coordinate ID) bases with quality value exceeded 30
MID Q30
Ratio of MID (Molecule ID) bases with quality value exceeded 30
Total Reads
1,299,371,915
Total Q30
82.55%
CID Q30
88.33%
MID Q30
85.65%
Annotation
Exonic
Number of reads that mapped uniquely to an exonic region and on the same strand of the genome
Intronic
Number of reads that mapped uniquely to an intronic region and on the same strand of the genome
Intergenic
Number of reads that mapped uniquely to an intergenic region and on the same strand of the genome
Transcriptome
Number of reads that mapped to a unique gene in the transcriptome. These reads are considered for MID counting. (Transcriptome = Exonic + Intronic)
Antisense
Number of reads mapped to the transcriptome but on the opposite strand of their annotated gene
Exonic
360,653,186
Intronic
58,457,788
Intergenic
141,115,742
Transcriptome
419,110,974
Antisense
122,900,040
RNA Mapping
Clean Reads
Number of Valid CID Reads that have passed QC
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Clean Reads
852,423,959
Uniquely Mapped Reads
560,226,716
Multi-Mapped Reads
211,588,387
Unmapped Reads
80,608,856
Tissue
DNB Under Tissue
Number of DNBs under tissue coverage region
mRNA-Captured DNBs Under Tissue
Number of DNBs under tissue that have captured mRNA
Genes Under Tissue
Number of detected gene under tissue coverage
Number of MID Under Tissue Coverage
Number of MID under tissue coverage
Fraction MID in Spots Under Tissue
Fraction of MID under tissue over total unique reads (MID Under Tissue / Unique Reads)
Reads Under Tissue
Number of reads with position prior to filtration under tissue coverage
Fraction Reads in Spots Under Tissue
Fraction of mapped reads under tissue over total mapped reads (Mapped Reads in Spots Under Tissue / (Valid CID Reads + Discarded MID Reads))
DNB Under Tissue
26,483,222
mRNA-Captured DNBs Under Tissue
9,481,859
Genes Under Tissue
22,848
Number of MID Under Tissue Coverage
21,190,353
Fraction MID in Spots Under Tissue
58.42%
Reads Under Tissue
512,269,047
Fraction Reads in Spots Under Tissue
49.85%
Sequencing Saturation
(left) Plot of the sequencing saturation as a function of sequencing depth(bin200)
(middle) Plot of the median number of genes detected per bin as a function of sequencing depth(bin200)
(right) Plot of the unique reads detected per bin as a function of sequencing depth(bin200)
Tissue Square Bin Statistics
Bin Size
The size of Bin which is the unit of aggregated DNBs in a squared region (i.e. Bin 50 = 50 * 50 DNBs)
Mean Reads (per bin)
Mean number of sequenced reads divided by the number of bins under tissue coverage
Median Reads (per bin)
Median number of sequenced reads divided by the number of bins under tissue coverage (pick the middle value after sorting)
Mean Gene Type (per bin)
Mean number of unique gene types divided by the number of bins under tissue coverage
Median Gene Type (per bin)
Median number of unique gene types divided by the number of bins under tissue coverage
Mean MID (per bin)
Mean number of MIDs divided by the number of bins under tissue coverage
Median MID (per bin)
Median number of MIDs divided by the number of bins under tissue coverage
Bin Size
Mean Reads
(per bin)
Median Reads
(per bin)
Mean Gene Type
(per bin)
Median Gene Type
(per bin)
Mean MID
(per bin)
Median MID
(per bin)
20
7,660
7,041
168
169
316
312
50
47,126
46,658
773
798
1,949
1,995
100
183,608
190,867
2,171
2,308
7,595
7,973
150
403,044
429,347
3,660
3,971
16,672
17,848
200
696,964
760,490
5,005
5,541
28,830
31,675
Bin 20
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 50
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 100
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 150
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 200
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Clustering
(left) Clustering spots (bin200) under tissue covered with the Leiden algorithm
(right) UMAP projections of spots (bin200) colored by automated clustering. Same color is assigned to spots that are within shorter distance and with similar gene expression profile
Tissue Plot with Spots (bin200)
UMAP Projection of Spots (bin200)
Cell Bin Statistics
Cell Count
Number of cells
Mean/Median Cell Area
Mean/Median cell area (pixel)
Mean/Median DNB Count
Mean/Median number of DNBs that have captured-mRNAs per cell
Mean/Median Gene Type
Mean/Median genes per cell
Mean/Median MID
Mean/Median MID count per cell
Cell Count
24,410
Mean Cell Area
240
Median Cell Area
215
Mean DNB Count
161
Median DNB Count
137
Mean Gene Type
119
Median Gene Type
105
Mean MID
224
Median MID
187
Cell Bin
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, DNB numbers, and cell area (pixel) with rug along the x axis
Clustering
(left) Clustering spots (cell bin) under tissue covered region with the Leiden algorithm
(right) UMAP projections of spots (cell bin) colored by automated clustering. Spots in the short distance are assigned with the same color have similar gene expression profile.
Tissue Plot with Spots (cell bin)
UMAP Projection of Spots (cellbin)
Image Information
Manufacture
motic
Model
MoticamProS5 Lite M
Scan Time
2022-1-20 15:1:34
Overlap
0.1
Exposure Time (ms)
11.795
Scan Rows
10
Scan Columns
8
FOV Height
2,035
FOV Width
2,436
Stain Type
ssDNA
Stitched Image
No
Image Name
SS200000154TR_F5_20221124_180305_1.1.3
Stitching
Template Source Row No.
The row number of the template FOV used for predicting the entire template
Template Source Column No.
The column number of the template FOV used for predicting the entire template
Global Height
Height of the stitched image
Global Width
Width of the stitched image
Template Source Row No.
0
Template Source Column No.
2
Global Height
18,523
Global Width
17,787
QC
ImageQC version
ImageQC version
QC Pass
Whether the image(s) passed imageQC quality check
Track Line Score
Reference score for track line detection
Clarity Score
Reference score for image clarity
Good FOV Count
Number of FOVs that have at least one track dot detected
Total FOV Count
Total number of FOVs
Stitching Score
Reference score for stitching
Tissue Segmentation Score
Reference score for tissue segmentation
Registration Score
Reference score for aligning image with gene expression matrix
ImageQC Version
1.1.3
QC Pass
Pass
Track Line Score
92
Clarity Score
71
Good FOV Count
74
Total FOV Count
80
Stitching Score
89
Tissue Segmentation Score
100
Registration Score
96
Registration
ScaleX
The lateral scaling between image and template
ScaleY
The longitudinal scaling between image and template
Rotation
The rotation angle of the image relative to the template
Flip
Whether the image is flipped horizontally
Image X Offset
Offset between image and matrix in x direction
Image Y Offset
Offset between image and matrix in y direction
Counter Clockwise Rotation
Counter clockwise rotation angle
Manual ScaleX
The lateral scaling based on image center (manual-registration)
Manual ScaleY
The longitudinal scaling based on image center (manual-registration)
Manual Rotation
The rotation angle based on image center (manual-registration)
Matrix X Start
Gene expression matrix offset in x direction by DNB numbers
Matrix Y Start
Gene expression matrix offset in y direction by DNB numbers
Matrix Height
Gene expression matrix height
Matrix Width
Gene expression matrix width
ScaleX
1.003
ScaleY
1.003
Rotation
0.858
Flip
True
Image X Offset
6,077
Image Y Offset
1,488
Manual ScaleX
-
Manual ScaleY
-
Manual Rotation
-
Counter Clockwise Rotation
90
Matrix X Offset
2.00
Matrix Y Offset
7.00
Matrix Height
26,458
Matrix Width
26,452
Horizontal Image Stitching Deviation Heatmap
Image stitching deviation in the horizontal axis, a lighter color indicates better stitching (the heatmap and frame of axes have been adjusted with the registration parameters)
Vertical Image Stitching Deviation Heatmap
Image stitching deviation in the vertical axis, a lighter color indicates better stitching (the heatmap and frame of axes have been adjusted with the registration parameters)